NM_005334.3(HCFC1):c.2590G>A (p.Ala864Thr) AND Methylmalonic acidemia with homocystinuria, type cblX

Germline classification:: Benign (2 submissions)
Last evaluated:: Jan 28, 2024
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000602586.9

Allele description [Variation Report for NM_005334.3(HCFC1):c.2590G>A (p.Ala864Thr)]

NM_005334.3(HCFC1):c.2590G>A (p.Ala864Thr)

Gene:

HCFC1:host cell factor C1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xq28

Genomic location:

Preferred name:

NM_005334.3(HCFC1):c.2590G>A (p.Ala864Thr)

HGVS:

NC_000023.11:g.153956670C>T
NG_012513.1:g.19699G>A
NM_005334.3:c.2590G>AMANE SELECT
NP_005325.2:p.Ala864Thr
NC_000023.10:g.153222121C>T
NM_005334.2:c.2590G>A

Protein change:

A864T

Links:

dbSNP: rs190023981

NCBI 1000 Genomes Browser:

rs190023981

Molecular consequence:

NM_005334.3:c.2590G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Methylmalonic acidemia with homocystinuria, type cblX (MAHCX)
Synonyms:: INTELLECTUAL DEVELOPMENTAL DISORDER, X-LINKED 3
Identifiers:: MONDO: MONDO:0010657; MedGen: C0796208; Orphanet: 369962; OMIM: 309541

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000734763	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus	no assertion criteria provided	Likely benign	germline	clinical testing
SCV001114915	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Jan 28, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000734763

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus

no assertion criteria provided

Likely benign

germline

clinical testing

SCV001114915

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Jan 28, 2024)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV000734763.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Invitae, SCV001114915.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Mar 16, 2024

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